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Crystal structure of ortho-aminophenol oxidase SmNspF from Streptomyces murayamaensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-D6RTB9-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.15 Mixing 5 microliter of SmNspF solution (10 mg/ml) with 4 microliter of reservoir solution (8% PEG 8000, and 800.0 mM Lithiumsulfate , 20.0 mM TRIS, 16.1 mM HCl)
Crystal Properties Matthews coefficient Solvent content 2.64 53.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.189 α = 90 b = 86.189 β = 90 c = 88.245 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 4M Vertical CRL / Horizontal Eliptical mirror 2022-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 12.812 keV ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.95 74.64 99.1 0.919 2.4 3.7 52735 46.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 0.059
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.4 74.64 28394 1416 98.958 0.186 0.1827 0.2376 0.2077 RANDOM 60.948
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 17.579 17.579 -35.157
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.531 r_dihedral_angle_3_deg 14.898 r_dihedral_angle_6_deg 13.122 r_mcangle_it 10.757 r_scangle_it 10.216 r_dihedral_angle_1_deg 7.744 r_mcbond_it 7.695 r_scbond_it 7.497 r_dihedral_angle_2_deg 6.334 r_angle_refined_deg 1.969
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.531 r_dihedral_angle_3_deg 14.898 r_dihedral_angle_6_deg 13.122 r_mcangle_it 10.757 r_scangle_it 10.216 r_dihedral_angle_1_deg 7.744 r_mcbond_it 7.695 r_scbond_it 7.497 r_dihedral_angle_2_deg 6.334 r_angle_refined_deg 1.969 r_nbtor_refined 0.291 r_nbd_refined 0.195 r_symmetry_nbd_refined 0.181 r_ncsr_local_group_1 0.141 r_xyhbond_nbd_refined 0.132 r_symmetry_xyhbond_nbd_refined 0.128 r_chiral_restr 0.096 r_gen_planes_refined 0.011 r_bond_refined_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4977 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement Aimless data scaling gemmi data extraction autoPROC data reduction MOLREP phasing